Fig. 3: Assembly of reference transcriptomes enables the measurement of molecular wound responses in both acoel and algal cells.

a Tails at 0, 3, and 6 hpa and heads at 0 hpa were collected for long and short read RNA sequencing to assemble reference transcriptomes de novo for both the acoel and the alga. Three replicates were obtained from 0 and 3 hpa tails, two from 6 hpa, and one from 0 hpa heads, with each replicate containing 5 animals. b Experimental design for identifying the species origin of transcripts through sequencing the DNA extracted from acoel-enriched and alga-enriched samples. c Sequencing depth of each transcript in the acoel-enriched and alga-enriched samples. Dotted lines indicate the gates used to assign acoel (blue) and algal (green) origin. The percentage of transcripts classified in each category is shown. Chloroplastic transcripts are annotated based on their high abundance in the alga-enriched sample and GO term predictions (cellular component GO term: 0009507 or 0009535, localized in chloroplast). d Fractions of acoel (blue) and algal (green) reads are consistent across samples and treatments, based on the Illumina short-read sequencing of tail samples specified in (a). Boxes represent upper and lower quartiles with the median marked by the middle line, the bars represent the upper and lower fences. Number of DEGs in acoel (e) and algae (f) at different time points post amputation (log₂FoldChange \(\geqq\) 0.8 or \(\leqq\) −0.8, p-adj \(\leqq\) 0.05, calculated with DESEQ2 using Wald test followed by Benjamini and Hochberg correction). Red: upregulated genes; blue: downregulated genes. Schematics are created with BioRender.com.